Oh, absolutely. I believe the idea is that the app settings inside Settings are supposed to be settings you rarely change, but the division was never very well thought out, and it’s been neglected for years, not in the least because any third party app putting its settings there was denied Harbour access. However, the fact that they’ve made it prominently visible again and put new settings in there makes me believe they’re working on making it more logical.
I suppose they could eventually decide to make the app settings inside Settings work a bit like dconf-editor, where every application setting can be found and modified without needing the application itself to be running. The easiest way to do thing would probably be to let developers put absolutely everything inside Settings, and put whatever they want inside their application, which could be everything found inside Settings or just a subset of those.